RUI: Atomistic Simulations of Lipid Bilayer Membranes

Wabash College, Crawfordsville IN

Investigators

Abstract

Molecular dynamics simulations will be carried out on membranes containing a variety of phospholipids, as well as small solutes, sterols, peptides, and trans-membrane proteins. These types of membranes are inherently disordered in the physiologically relevant liquid-crystalline phase, thus atomic-level structural data is difficult to obtain experimentally. These simulations will complement the existing body of experimental data, e.g., comparison will be made between properties observed in the simulation and those obtained experimentally in order to test the validity of the work and possibly to reconsider previous interpretations of the data. Specifically, many of the analyses for these simulations have as their goal the extraction of bilayer properties that aid in the interpretation of experiment. Specific scientific aims of this research include the characterization of material properties of lipid bilayers containing polyunsaturated fatty acids, a description of interactions between polyunsaturated fatty acids and the transmembrane proteins rhodopsin and peripheral cannabinoid receptor CB2, the investigation of detailed molecular structures in sterol/lipid mixtures relevant to raft formation, and the development of methods for the accurate simulation of membrane systems. To carry out these projects, carefully planned simulations, of hundreds of nanoseconds in length, will be carried out using a Beowulf-style parallel computer that will be upgraded and expanded. This research program will have significant impact on undergraduate instruction through the transfer of molecular modeling techniques from the research laboratory to the chemistry curriculum at Wabash College, as well as via the research internships that will be available to numerous students during the academic year and summer. In addition to testing simulation methods, carrying out simulations, and analyzing/interpreting simulation results, students will present their results to the campus community and at national and regional scientific meetings. These presentations will prepare them for careers as scientific researchers and will demonstrate exciting opportunities available to prospective science majors.